3T8K | pdb_00003t8k

The crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b

• PDB DOI: https://doi.org/10.2210/pdb3T8K/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Leptotrichia buccalis C-1013-b
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-08-31 
• Deposition Author(s): Tan, K., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.215 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

The crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b

Tan, K., Bigelow, L., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.54 kDa 
• Atom Count: 3,326 
• Modeled Residue Count: 367 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	186	Leptotrichia buccalis C-1013-b	Mutation(s): 0  Gene Names: Lebu_0176
UniProt
Find proteins for C7NDE2 (Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b)) Explore C7NDE2  Go to UniProtKB:  C7NDE2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.215 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.193	α = 90
b = 101.019	β = 90
c = 108.184	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Tan, K., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary